Sequence scheduling and sample distribution techniques

ABSTRACT

A technique is disclosed for sample management for use in conjunction with sequencing devices that sequence biological samples, e.g., DNA and RNA. A sequencing device or a network of sequencing devices may be scheduled according to the characteristics of the samples in queue and the capabilities and availability of sequencing devices. Biological samples may be automatically queued and loaded via a sample distribution system. A sample distribution system may be used to reduce operator intervention.

BACKGROUND

The present disclosure relates generally to the field of geneticsequencing. More particularly, the disclosure relates to improvedtechniques for throughput of automating sequencing of genetic materialsby use of automated scheduling and/or automated sample distribution.

Genetic sequencing has become an increasingly important area of geneticresearch, promising future uses in diagnostic and other applications. Ingeneral, genetic sequencing consists of determining the order ofnucleotides for a nucleic acid such as a fragment of RNA or DNA.Relatively short sequences are typically analyzed, and the resultingsequence information may be used in various bioinformatics methods toalign fragments against a reference sequence or to logically fitfragments together so as to reliably determine the sequence of much moreextensive lengths of genetic material from which the fragments werederived. Automated, computer-based examination of characteristicfragments have been developed, and have been used more recently ingenome mapping, analysis of genetic variation between individuals,identification of genes and their function, and so forth. However,existing techniques are highly time-intensive, and resulting genomicinformation is accordingly extremely costly.

A number of alternative sequencing techniques are presently underinvestigation and development. These include the use of microarrays ofgenetic material that can be manipulated so as to permit paralleldetection of the ordering of nucleotides in a multitude of fragments ofgenetic material. The arrays typically include many sites formed ordisposed on a substrate. Additional materials, typically singlenucleotides or strands of nucleotides (oligonucleotides), are introducedand permitted or encouraged to bind to the template of genetic materialto be sequenced, thereby selectively marking the template in a sequencedependent manner. Sequence information may then be gathered by imagingthe sites. In certain current techniques, for example, each nucleotidetype is tagged with a fluorescent tag or dye that permits analysis ofthe nucleotide attached at a particular site to be determined byanalysis of image data.

Although such techniques show promise for significantly improvingthroughput and reducing the cost of sequencing, further progress in theparallelization, speed and reliability of sequencing is desirable.

BRIEF DESCRIPTION

The present disclosure provides significant improvements in the field ofnucleic acid sequencing, especially with regard to biological samplemanagement methods. The techniques may be used for high throughputsequencing, and will typically be most useful in sequencing of DNA andRNA (including cDNA). However, the biological sample distribution and/orscheduling techniques may be used for any suitable type of sampleanalysis devices. In certain embodiments, the techniques may be usedwith a variety of sequencing approaches or technologies, includingtechniques often referred to as sequencing-by-synthesis (SBS),sequencing-by-ligation, pyrosequencing, nanopore sequencing and soforth. The present techniques have been found or are believed to providefor more highly automated or higher quality sequencing, permittinghigher throughput and ultimately reduced sequence costs by providingimproved scheduling and decreased downtime for sequencing devices.Further, the techniques facilitate improved sample loading or queuing.

In one embodiment, the present disclosure provides a novel approach forscheduling sequencing runs for a group or network of sequencing devices.For example, such a group or network may be located in a high throughputsequencing lab or a core sequencing facility. Sequencing devicesrepresent large capital investments, and optimized scheduling ofsequencing runs (e.g., sample processing, data collection, and/oranalysis) avoids idle time on a sequencer and loss of resources. Thetechniques relate to a controller or processor-based device that assignsbiological samples to sequencing devices based on parameters associatedwith the sample (e.g., type of assay to be performed, a prioritydesignation) and parameters associated with the sequencing device (e.g.,estimated availability, sequencing capabilities). The processor-baseddevice accesses the relevant data and creates a sequencing schedule,including sample assignments to particular devices. The sequencingschedule is dynamic and changes according to the new information fromnewly added samples in the queue. For example, a higher priority samplemay jump in the line over a lower priority sample. In particularembodiments, the sequencing schedule may include an assessment ofin-progress sequencing. Certain sequencing runs may have collectedsufficient data to assemble a sequence even if the sequencing run is notyet complete. In one example, such runs may be interrupted and theassociated sequencing device reassigned to another biological sample tooptimize use of the sequencing device. In another example, a sequencingdevice that is underutilized may be assigned another biological sampleto be loaded into an in-progress run that is not interrupted for the newsample. Instead, the new sample is sequenced together with thein-progress sample. In a third example, the priority of a sample in aqueue may be raised or lowered based on sequencing data obtained on asequencing device in the network or group of devices. In such cases, twoor more samples may be related and the results from a first sample mayindicate that analysis of a second, related sample should be carried outon a more expedited basis that previously determined (or conversely on alower priority basis than a third sample).

The present techniques also involve networked or distributed control ofa plurality of sequencing devices to optimize the performance of thenetwork as a whole. In certain embodiments, the network may be astar-type arrangement with a central controller. In other embodiments,the network may be a ring-type arrangement in which the controllerresides on one or more of the networked sequencing devices. Regardlessof the particular arrangement, the sequencing devices may be controlledor scheduled such that particular devices are in use at particular timeswith the goal of adjusting the processing load of the network. In oneembodiment, the controller arbitrates between local processing andcloud-based processing of the sequencing data based on an estimatedprocessing load for the network.

In another embodiment, the present techniques include a sampledistribution system that is configured to facilitate sample loading intoone or more sequencing devices. As opposed to techniques in whichbiological samples are loaded by hand into a device, the sampledistribution system may provide automatic loading from a central samplestation and under processor-based control. Further, the sampledistribution system may be implemented as a plug-and-play arrangementthat works with a variety of sequencing devices. In one embodiment, thesample distribution system is provided as a backplane arrangement thatworks in conjunction with a sequencing device rack. The sampledistribution system may be integrated with the sequencing schedulingtechniques as provided herein. That is, the instructions for loading thesamples may be provided by the sequencing scheduling system. In otherembodiments, the sample distribution system may be provided as astandalone system with a user interface to provide loading instructions.

The present disclosure provides a system for scheduling sequencing runsfor a plurality of biological samples. The system includes a memorycircuit including executable application instructions and a processorconfigured to execute the application instructions. The processor isconfigured to execute instructions for receiving information related toavailability of the plurality of sequencing devices; receivingidentification information for a plurality of biological samples,wherein the identification information comprises sequencing parametersand a priority designation; assigning each of the plurality ofbiological samples to respective sequencing devices based at least inpart on the availability of each respective sequencing device and thesequencing parameters and the priority designation of each respectivesample; and providing an indication that one of the plurality ofbiological samples is ready to be sequenced based on an availability ofan assigned sequencing device.

The present disclosure also provides a sequencing device that includes amodule configured to acquire digitized signal data from a firstbiological sample during a sequencing run. The sequencing device alsoincludes at least one processor configured to: receive the digitizedsignal data; determine nucleotide identities of the first biologicalsample based on the digitized signal data; output one or more filescomprising the nucleotide identities; analyze the nucleotide identitiesto determine if enough digitized signal data has been acquired from thefirst biological sample; communicate that the sequencing device isavailable when enough digitized signal data has been acquired from thefirst biological sample while the module is acquiring additionaldigitized signal data from the first biological sample; and receive anindication that the sequencing run will be interrupted and thesequencing reassigned to a second biological sample when the sequencingdevice is available.

The present disclosure also provides a sample distribution system. Thesample distribution system includes a sample rack for storing aplurality of individual biological samples; a plurality of conduitsconfigured to couple to each respective biological sample and totransfer each respective biological sample within the system; a sampleinlet path in fluid communication with a sample loading port of abiological analysis device; a valve that controls fluid communicationbetween the plurality of conduits and the sample inlet path such thatonly one conduit of the plurality of conduits is in communication withthe sample inlet path at a given time and such that the biologicalsample coupled to the only one conduit is in fluid communication withthe sample loading port via the sample inlet path; and a controllercoupled to the valve and configured to receive instructions to load abiological sample into the biological analysis device and open a fluidcommunication pathway between a conduit coupled to the biological sampleand the sample loading port.

The present disclosure also includes a sequencing network. Thesequencing network includes a plurality of sequencing devices configuredto acquire digitized signal data from a biological sample during asequencing run and communicate information about the sequencing run. Thesequencing network also includes a controller coupled to the pluralityof sequencing devices, wherein the controller comprises: a memorycircuit including executable application instructions stored therein;and a processor configured to execute the application instructionsstored in the memory device, wherein the application instructioncomprise instructions for: receiving the information related tosequencing run for each respective sequencing device; receivingidentification information for a plurality of biological samples,wherein the identification information comprises sequencing parametersand a priority designation; and assigning each of the plurality ofbiological samples to respective sequencing devices based at least inpart on the information related to sequencing run of each respectivesequencing device and the sequencing parameters and the prioritydesignation of each respective sample.

The present disclosure provides a system for scheduling sequencing runsfor a plurality of biological samples. The system includes a memorycircuit including executable application instructions stored therein;and a processor configured to execute the application instructionsstored in the memory device, wherein the application instructionscomprise instructions for: receiving information related to sequencingcapability of the plurality of sequencing devices; receivingidentification information for a plurality of biological samples,wherein the identification information comprises sequencing parametersand a priority designation; assigning each of the plurality ofbiological samples to respective sequencing devices based at least inpart on the sequencing capability of each respective sequencing deviceand the sequencing parameters and the priority designation of eachrespective sample; and providing an indication that one of the pluralityof biological samples is ready to be sequenced based on an a sequencingcapability of an assigned sequencing device.

Embodiments of the present techniques are described herein by referenceto biological samples for a sequencing device. The disclosure is not,however, limited by the advantages of the aforementioned embodiment. Thepresent techniques may also be applied to devices capable of generatingother types of high throughput biological data, such as microarray dataor library screening data (e.g. from screening candidate drugs or fromscreening engineered protein variants).

DRAWINGS

These and other features, aspects, and advantages of the presentinvention will become better understood when the following detaileddescription is read with reference to the accompanying drawings in whichlike characters represent like parts throughout the drawings, wherein:

FIG. 1 is a diagrammatical overview of a sequencing system incorporatingaspects of the present technique;

FIG. 2 is a diagrammatical overview of a sequencing device that may beused in conjunction with the system of the type discussed with referenceto FIG. 1;

FIG. 3 is a perspective view of a sequencing device including a samplecartridge that may be used in conjunction with the system of the typediscussed with reference to FIG. 1;

FIG. 4 is a flow diagram of a method of interaction between a sequencingdevice and a scheduling controller that may be performed in conjunctionwith the system discussed with reference to FIG. 1;

FIG. 5 is a flow diagram of a method of interaction between a pluralityof sequencing devices and a scheduling controller that may be performedin conjunction with the system discussed with reference to FIG. 1;

FIG. 6 is a flow diagram of a method of generating a sequencing sampleschedule that may be performed in conjunction with the system discussedwith reference to FIG. 1;

FIG. 7 is a flow diagram of a method of generating a sequencing sampleschedule that may be performed in conjunction with the system discussedwith reference to FIG. 1;

FIG. 8 is a flow diagram of a method of distributing sample analysisthat may be performed in conjunction with the system discussed withreference to FIG. 1;

FIG. 9 is a diagrammatical overview of a sample distribution systemincorporating aspects of the present technique;

FIG. 10 is a diagrammatical overview of a sample distribution systemincluding a rack-based sequencing system incorporating aspects of thepresent technique; and

FIG. 11 is a perspective view of a plug-and-play backplane that may beused in conjunction with the system discussed with reference to FIG. 9.

DETAILED DESCRIPTION

The following detailed description of certain embodiments will be betterunderstood when read in conjunction with the appended drawings. To theextent that the figures illustrate diagrams of the functional blocks ofvarious embodiments, the functional blocks are not necessarilyindicative of the division between hardware circuitry. Thus, forexample, one or more of the functional blocks (e.g., processors ormemories) may be implemented in a single piece of hardware (e.g., ageneral purpose signal processor or random access memory, hard disk, orthe like). Similarly, the programs may be stand alone programs, may beincorporated as subroutines in an operating system, may be functions inan installed software package, and the like. It should be understoodthat the various embodiments are not limited to the arrangements andinstrumentality shown in the drawings.

Embodiments described herein may be used in various biological orchemical processes and systems for academic or commercial analysis. Morespecifically, embodiments described herein may be used in variousprocesses and systems where it is desired to detect an event, property,quality, or characteristic that is indicative of a desired reaction.

As used herein, an element or step recited in the singular and proceededwith the word “a” or “an” should be understood as not excluding pluralof said elements or steps, unless such exclusion is explicitly stated.Furthermore, references to “one embodiment” are not intended to beinterpreted as excluding the existence of additional embodiments thatalso incorporate the recited features. Moreover, unless explicitlystated to the contrary, embodiments “comprising” or “having” an elementor a plurality of elements having a particular property may includeadditional elements whether or not they have that property.

Turning now to the drawings, and referring first to FIG. 1, a managementsystem 10 for biological sample scheduling is illustrateddiagrammatically. The system 10 includes one or more controllers 12coupled to one or more sequencing devices 16 via suitable communicationslinks 18. The system 10 also includes an input for information relatedto samples 20 via communication link 22. For example, each individualsample 20 may include a barcode or RFID tag that communicates with thescheduling controller 12. The communication may occur via any suitablearrangement and protocol, such as via a local area network (LAN), ageneral wide area network (WAN), and/or a public network (e.g., theInternet) via the communications links 18 and 24. In other embodiments,some or all of the received data may be entered by a user, includingsample identification information. That is, the system 10 can beconfigured to receive data and information from various devices,including users of devices for generating biological data. Such data maybe used to assess the availability and/or capabilities of the associatedsequencing devices 16 to generate a sequencing schedule for samples thatneed to be analyzed. The data may also be used to generate a prioritydesignation for the samples waiting to be analyzed. As additionalsamples join the queue, the system is capable of receiving additionalinformation to create a dynamic schedule that may rearrange the proposedsequencing times if higher priority samples join the queue.

In embodiments in which there are multiple sequencing devices 16, thecontroller arrangement may be a star arrangement in which the sequencingdevices 16 all communicate with a central controller 12. Otherarrangements may include ring-based arrangement in which the controller12 resides on or is associated with one or more sequencing devices 16.That is, the functionality of the controller 12 may be incorporated intothe sequencing device 16. Further, the sequencing devices 16 maycommunicate with one another to distribute computing resources.

The scheduling controller 12 may be implemented as one or more of apersonal computer system, server computer system, thin client, thickclient, hand-held or laptop device, multiprocessor system,microprocessor-based system, set top box, programmable consumerelectronic, network PC, minicomputer system, smart phone (e.g. iPhone),tablet computer (e.g. iPad), mainframe computer system, and distributedcloud computing environments that include any of the above systems ordevices, and the like. The scheduling controller 12 may include one ormore processors or processing units 28, a memory architecture 32 thatmay include RAM 34 and non-volatile memory 36. The memory architecture32 may further include removable/non-removable, volatile/non-volatilecomputer system storage media. Further, the memory architecture 32 mayinclude one or more readers for reading from and writing to anon-removable, non-volatile magnetic media, such as a hard drive, amagnetic disk drive for reading from and writing to a removable,non-volatile magnetic disk (e.g., a “floppy disk”), and/or an opticaldisk drive for reading from or writing to a removable, non-volatileoptical disk such as a CD-ROM, DVD-ROM. The controller 12 may alsoinclude a variety of computer system readable media. Such media may beany available media that is accessible by the cloud computingenvironment, such as volatile and non-volatile media, and removable andnon-removable media.

The memory architecture 32 may include at least one program producthaving a set (e.g., at least one) of program modules implemented asexecutable instructions that are configured to carry out the functionsof the present techniques. For example, executable instructions 38 mayinclude an operating system, one or more application programs, otherprogram modules, and program data. Generally, program modules mayinclude routines, programs, objects, components, logic, data structures,and so on, that perform particular tasks or implement particularabstract data types. Program modules may carry out the functions and/ormethodologies of the techniques as described herein including, but notlimited to, scheduling management and/or sample distribution.

The components of the controller 12 may be coupled by an internal bus 39that may be implemented as one or more of any of several types of busstructures, including a memory bus or memory controller, a peripheralbus, an accelerated graphics port, and a processor or local bus usingany of a variety of bus architectures. By way of example, and notlimitation, such architectures include Industry Standard Architecture(ISA) bus, Micro Channel Architecture (MCA) bus, Enhanced ISA (EISA)bus, Video Electronics Standards Association (VESA) local bus, andPeripheral Component Interconnects (PCI) bus.

The controller may also communicate with one or more external devicessuch as a keyboard, a pointing device, a display 42, etc.; that enable auser to interact with the controller 12; and/or any devices (e.g.,network card, modem, etc.) that enable the controller 12 to communicatewith one or more other computing devices. Such communication can occurvia I/O interfaces 44. Still yet, the controller 12 may communicate withone or more networks such as a local area network (LAN), a general widearea network (WAN), a public network (e.g., the Internet), and/or acloud computing environment via a suitable network adapter.

As provided herein, the system 10 is configured to be used inconjunction with one or more devices that analyze biological samples 20.The system 10 provides a schedule for biological samples 20 to be loadedinto individual devices. The system 10 may generate a proposed schedulein which waiting samples 20 are assigned an estimated sequencing time(e.g., a time to be loaded) and are assigned to a particular device. Inthis manner, an operator may consult the generated schedule beforeloading samples 20 into the sequencing devices 16. The system 10 mayalso generate alarms or other indications to an operator. For example,when a scheduled sample 20 is ready to be loaded into an individualsequencing device 16, the system 10 may provide an alarm or otherindication to an operator. In one embodiment, the system 10 may send atext message to a pager or mobile device indicating that a sample 20 isready to be loaded. The system 10 may also acknowledge that a particularsample 20 has been loaded and update the schedule accordingly. In oneembodiment, the sample 20 is scanned before being loaded and the sampleinformation is stored by the controller 12. In another embodiment, anoperator may confirm that the sample 20 has been loaded. Althoughembodiments of the present disclosure are depicted in conjunction withsequencing devices, it should be understood that, in certainembodiments, the present techniques may be used in conjunction withother types of devices. Further, the present techniques may also be usedin conjunction with an automatic sample distribution system. In suchembodiments, the samples 20 are loaded without operator intervention.

The controller 12 may provide a user interface that guides an operatorthrough a series of setup options. For example, upon receiving a sample20, the operator may specify information about the sample 20 (desiredassay types, priority information, sample preparation information,patient information, organism, date or time of sample collection,location of sample collection, circumstances of sample collection,suspected sample characteristics, etc.) and may select from availablesequencing devices that may be appropriate. Accordingly, even though thecontroller 12 may be configured to match the sample 20 to the sequencingdevice 16 according to a rules-based protocol, the operator may also addconditions or parameters that override the protocol. For example, thesample 20 may be prepared according to a kit that is optimized for usewith sequencing devices from a particular manufacturer. In such anembodiment, the operator may specify the sample 20 should be matched tosequencing devices 16 from that manufacturer. In other embodiments, theuser interface may provide menu options that prompt user input withregard to particular sample preparation kits or tagging and use theinformation in the matching protocol.

FIG. 2 is a schematic diagram of the sequencing device 16 that may beused in conjunction with the system 10. The sequence device 16 may beimplemented according to any sequencing technique, such as thoseincorporating sequencing-by-synthesis methods described in U.S. PatentPublication Nos. 2007/0166705; 2006/0188901; 2006/0240439; 2006/0281109;2005/0100900; U.S. Pat. No. 7,057,026; WO 05/065814; WO 06/064199; WO07/010,251, the disclosures of which are incorporated herein byreference in their entireties. Alternatively, sequencing by ligationtechniques may be used in the sequencing device 16. Such techniques useDNA ligase to incorporate oligonucleotides and identify theincorporation of such oligonucleotides and are described in U.S. Pat.Nos. 6,969,488; 6,172,218; and 6,306,597; the disclosures of which areincorporated herein by reference in their entireties. Some embodimentscan utilize nanopore sequencing, whereby target nucleic acid strands, ornucleotides exonucleolytically removed from target nucleic acids, passthrough a nanopore. As the target nucleic acids or nucleotides passthrough the nanopore, each type of base can be identified, for example,by measuring fluctuations in the electrical conductance of the pore(U.S. Pat. No. 7,001,792; Soni & Meller, Clin. Chem. 53, 1996-2001(2007); Healy, Nanomed. 2, 459-481 (2007); and Cockroft, et al. J. Am.Chem. Soc. 130, 818-820 (2008), the disclosures of which areincorporated herein by reference in their entireties). Yet otherembodiments include detection of a proton released upon incorporation ofa nucleotide into an extension product. For example, sequencing based ondetection of released protons can use an electrical detector andassociated techniques that are commercially available from Ion Torrent(Guilford, Conn., a Life Technologies subsidiary) or sequencing methodsand systems described in US 2009/0026082 A1; US 2009/0127589 A1; US2010/0137143 A1; or US 2010/0282617 A1, each of which is incorporatedherein by reference in its entirety. Particular embodiments can utilizemethods involving the real-time monitoring of DNA polymerase activity.Nucleotide incorporations can be detected through fluorescence resonanceenergy transfer (FRET) interactions between a fluorophore-bearingpolymerase and γ-phosphate-labeled nucleotides, or with zeromodewaveguides as described, for example, in Levene et al. Science 299,682-686 (2003); Lundquist et al. Opt. Lett. 33, 1026-1028 (2008);Korlach et al. Proc. Natl. Acad. Sci. USA 105, 1176-1181 (2008), thedisclosures of which are incorporated herein by reference in theirentireties. Other suitable alternative techniques include, for example,fluorescent in situ sequencing (FISSEQ), and Massively ParallelSignature Sequencing (MPSS). In particular embodiments, the sequencingdevice 16 may be a HiSeq, MiSeq, or HiScanSQ from Illumina (San Diego,Calif.).

Different types of sequencing devices can provide different advantagesand disadvantages. For example, different sequencing devices vary in rawread length (e.g. length of contiguous nucleotide positions that aredetermined for a given nucleic acid fragment in a single instrumentrun), raw read accuracy (e.g. probability of an error occurring in theread of a particular nucleic acid fragment), depth of sequencingprovided per run (e.g. number of nucleic acid fragments read in a run),accuracy in determining the length of homopolymeric regions, andaccuracy in reading sequence regions having particular compositions(e.g. GC rich regions vs. AT rich regions). An advantage of having avariety of types of sequencing devices in a network or group ofsequencing devices is that a particular device can be selected to suit adesired inquiry. For example, in an application where overall accuracyis of paramount importance it may be desirable to select a sequencerthat provides a high depth of sequencing (which results in increasedaccuracy after data analysis) even if this means using a device that hasshorter overall read length. Alternatively, for de novo genomesequencing applications it may be more desirable to select a sequencerthat generates longer read lengths even if the selected device is notthe most accurate in the network. Of course a particular sample can besequenced on multiple types of sequencing devices to obtain the combinedbenefits of more than one device.

In accordance with the systems and methods set forth herein, particularsamples can be prioritized for use on a certain type of sequencer basedon sample characteristics, data quality (or quantity) expectations etc.A change can be made in this priority for a particular sample in a queuebased on data obtained for a related or similar sample. For example,several related samples can be initially slated for sequencing on afirst device that generates longer read lengths than a second device butthat is not as accurate at determining homopolymer lengths as the seconddevice. In the event that sequencing of one of the samples indicates thepresence of homopolymer regions of interest, the priority of the relatedsamples in the queue can be changed to shunt them to the secondsequencing device where more accurate reads of homopolymer regions canbe obtained. Similarly, several related samples can be initiallyprioritized for evaluation using a particular protocol (which, incertain embodiments, may include preset, user modified, or customprotocols), and the priority for samples in the queue for that protocolcan be modified based on results obtained for one of the samples. Forexample, samples that were initially designated for a relatively timeconsuming, deep sequencing protocol can be re-designated for a lowerdepth and faster protocol if the results from a first sample indicate anurgent need to get preliminary data. Such a situation can arise forexample, if it becomes apparent from sequencing data that the firstsample contained a fast acting pathogen that should be rapidly diagnosedin the other samples. In one example, a sequencing run may determine isa sample is positive for salmonella DNA. The runs may proceed untilidentification is possible.

In one embodiment, the sample priority may be based on a desired errorrate. That is, certain samples may have a wider tolerance of acceptableerror rates (depending on the end use of the sequencing data), and maybe scheduled on a wider array of assays and/or devices relative to asample with more stringent or lower error rate specifications (e.g.,forensic samples). For example, an estimated potential error rate may berelated to the number of reads and/or the length of the reads as well asthe number of cycles. In another embodiment, a run may be continueduntil a determination is made that an error rate is too high foradequate data analysis.

The disclosed techniques may also incorporate scheduling or assignmentinformation for other types of analysis devices or orthogonal techniques(purification, chromatography, SNP analysis, etc, antibody or PCR-basedtechniques). Further, the sequencing runs may be followed by arecommended or independent validation step

In the depicted embodiment, the sequencing device 16 includes a separatesample processing device 50 and an associated computer 52. However,these may be implemented as a single device. Further, the associatedcomputer 52 may be local to or networked with the sample processingdevice 50. The devices may include identification components, such asbarcodes or RFID tags, that facilitate identification of users, samples,and/or devices. In other embodiments, the computer 52 may be capable ofcommunicating with a cloud computing environment that is remote from thesequencing device 16. That is, the computer 52 may be capable ofcommunicating with the sequencing device 16 through the cloud computingenvironment. In the depicted embodiment, the biological sample may beloaded into the sample processing device 50 as a sample slide 70 that isdetected to generate sequence data. For example, reagents that interactwith the biological sample may fluoresce at particular wavelengths inresponse to an excitation beam generated by a detection module 72 andthereby return radiation for imaging. For instance, the fluorescentcomponents may be generated by fluorescently tagged nucleic acids thathybridize to complementary molecules of the components or tofluorescently tagged nucleotides that are incorporated into anoligonucleotide using a polymerase. As will be appreciated by thoseskilled in the art, the wavelength at which the dyes of the sample areexcited and the wavelength at which they fluoresce will depend upon theabsorption and emission spectra of the specific dyes. Such returnedradiation may propagate back through the directing optics. Thisretrobeam may generally be directed toward detection optics of thedetection module 72. Although the system of FIG. 2 is exemplified inregard to an optical imaging detector, it will be understood that otherdetectors can be used. The detection module can be physically separatedfrom the sample slide, for example via an optical train used in manyimaging devices. Alternatively, the detection module can be integratedwith the slide (or other sample carrier), for example, as is the casefor nanopore sequencing devices and CMOS-based proton detection devicesset forth previously herein including in the incorporated references.

Taking the example of optical detection systems, the imaging moduledetection optics may be based upon any suitable technology, and may be,for example, a charged coupled device (CCD) sensor that generatespixilated image data based upon photons impacting locations in thedevice. However, it will be understood that any of a variety of otherdetectors may also be used including, but not limited to, a detectorarray configured for time delay integration (TDI) operation, acomplementary metal oxide semiconductor (CMOS) detector, an avalanchephotodiode (APD) detector, a Geiger-mode photon counter, or any othersuitable detector. TDI mode detection can be coupled with line scanningas described in U.S. Pat. No. 7,329,860, which is incorporated herein byreference. Other useful detectors are described, for example, in thereferences provided previously herein in the context of various nucleicacid sequencing methodologies.

The detection module 72 may be under processor control, e.g., via aprocessor 74, and the sample receiving device 18 may also include I/Ocontrols 76, an internal bus 78, non-volatile memory 80, RAM 82 and anyother memory structure such that the memory is capable of storingexecutable instructions, and other suitable hardware components that maybe similar to those described with regard to FIG. 2. Further, theassociated computer 20 may also include a processor 84, I/O controls 86,a communications module 87, and a memory architecture including RAM 88and non-volatile memory 90, such that the memory architecture is capableof storing executable instructions 92. The hardware components may belinked by an internal bus 94, which may also link to the display 96. Inembodiments in which the sequencing device 16 is implemented as anall-in-one device, certain redundant hardware elements may beeliminated. Further, the sequencing device 16 may also interact with thecloud computing environment. Such embodiments may be beneficial fordistributing processing load for the system 10.

The system 10 may include multiple sequencing devices 16, each with thesame or different capabilities. That is, the sequencing devices 16 maybe capable of performing different types of assays or sequencing runs,including DNA sequencing, RNA sequencing, genotyping, SNP testing, CNVanalysis, methylation analysis, gene expression analysis, agrigenomics,cytogenetics, and/or cancer genomics. Further, devices with similarassay capabilities (e.g., DNA sequencing) may perform at differentspeeds, with different resolution, and with different sample preparationspecifications. The system 10 may be capable of tracking suchdifferences to assign the sample 20 to the appropriate sequencing device16. In particular embodiments, the devices 16 may operate with acartridge system that allows the devices to switch assay capabilitiesvia the changing out of internal cartridges. Certain other componentsare associated with a device housing and are interoperable with avariety of cartridges. In this manner, each device 16, when available,may offer a range of assay capabilities depending on the characteristicsof the inserted cartridge.

FIG. 3 shows an exemplary sequencing device 16 that incorporates acartridge 100 that is configured to be inserted into a housing 102. Thecartridge 100 exploits advantages of integrated optoelectronics andcartridge-based fluidics that are provided by several embodiments setforth herein. The housing 102 contains various fixed componentsincluding, for example, optical components, computational components,power source, fan and the like. A screen 103 present, for example, onthe front face of the housing 102 functions as a graphical userinterface that can provide various types of information such asoperational status, status of an analytical procedure (e.g. a sequencingrun) being carried out, status of data transfer to or from the device16, instructions for use, warnings or the like. A cartridge receptacle104 is also present on the front face of the housing 102. As shown, thecartridge receptacle 104 can be configured as a slot having a protectivedoor 105. A status indicator 106, in the form of an indicator light onthe frame of the cartridge receptacle in this example, is present andcan be configured to indicate the presence or absence of a cartridge inthe device 16. For example the indicator light 106 can change from on tooff or from one color to another to indicate presence or absence of acartridge. A power control button 107 is present on the front face ofthe housing 102 in this example as is identifying indicia 108 such asthe name of the manufacturer or instrument. In particular embodiments,the cartridge 100 may include an identification element thatcommunicates via handshake with the housing 102 to confirm that thecartridge is compatible with the processing elements available in thehousing 102.

The cartridge 100 can be used to provide a sample and reagents to thedevice 16. The fluidic cartridge 100 includes a housing 111 thatprotects various fluidic components such as reservoirs, fluidicconnections, pumps, valves and the like. A flow cell 112 is integratedinto the fluidic cartridge in a position where it is in fluidcommunication with reagents within the housing. The housing 111 has anopening 113 through which a face of the flow cell 112 is exposed suchthat it can interact optically with the optical scanning device when thefluidic cartridge 100 is placed in the cartridge receptacle 104. Thecartridge housing 111 also includes a sample port 114 for introductionof a target nucleic acid sample. A bar code 115 or other machinereadable indicia can optionally be present on the cartridge housing 111,for example, to provide assay capability tracking and management. Otherindicia 116 can also be present on the housing for convenientidentification by a human user, for example, to identify themanufacturer, analytical analysis supported by the fluidic cartridge,lot number, expiration date, safety warnings and the like. The apparatusshown in FIG. 3 is exemplary.

In some embodiments, the cartridge 100 may include additional features,such as the light source (e.g., LEDs) that are configured to provideexcitation light to the reactions sites of the biosensor. The cartridge100 may also include a fluidic storage system (e.g., storage forreagents, sample, and buffer) and a fluidic control system (e.g., pumps,valves, and the like) for fluidically transporting reaction components,sample, and the like to the reaction sites. For example, after thebiosensor component of the cartridge is prepared or manufactured, thebiosensor may be coupled to a housing or container of the cartridge. Insome embodiments, the cartridges 100 may be self-contained, disposableunits. However, other embodiments may include an assembly with removableparts that allow a user to access an interior of the cartridge 100 formaintenance or replacement of components or samples. The cartridge 100may be removably coupled or engaged to larger bioassay systems, such asa sequencing system, that conducts controlled reactions therein.

FIG. 4 is a process flow diagram illustrating a method of sequencingschedule management in accordance with some embodiments. The method isgenerally indicated by reference number 150 and includes various stepsor actions represented by blocks. It should be noted that the method 150may be performed as an automated procedure by a system, such as system10. Further, certain steps or portions of the method may be performed bya single device (e.g., a controller 12) or by separate devices (e.g. acontroller 12 and a sequencing device 16). In embodiments, the method150 may be performed periodically as new information or samples enterthe system 10 or as samples exit the system 10.

According to the exemplary embodiment illustrated, the method 150 beginswith the steps of receiving sequencing device information at block 152and receiving sample information at block 154. The sequencing deviceinformation may include one or more of: identification information(e.g., manufacturer, model number) for a sequencing device 16, assaycapability information, information about samples that have been loadedinto a particular sequencing device 16, estimated availability of asequencing device 16, and sequencing data. In certain embodiments,certain information about the sequencing devices 16 (e.g., assaycapability information) may be stored on the controller 12 and looked upin response to receiving identification information from a particulardevice 16. For sequencing devices 16 that incorporate a cartridge 100,block 152 may also include information about the assay capabilities ofany inserted cartridge 100. The sample information may includeidentification information (e.g., patient information), sample type,preparation information, desired assay types, and a priority designation(e.g., high priority, default or medium priority, low priority). Themethod 150 assigns the sample to a sequencing device 16 based on a bestmatch between the sequencing device information and the sampleinformation at block 158.

The controller 12 may use any appropriate algorithm or technique formatching a sample to a sequencing device 16 based on the availablecriteria. Such algorithms may implement Bayesian optimizationalgorithms, heuristic approaches, colony optimization algorithms,genetic algorithms, Monte Carlo modeling, and/or weighted approaches.Matching solutions may be optimized with a goal that any particularsequencing device 16 is operating on a continuous flow basis. Otherconstraints may include null solutions when the assay capabilities of asequencing device 16 do not match the desired assays for the sample.

At block 159, the method 150 provides an indication that the sample isready to be sequenced and/or is assigned to a particular sequencingdevice 16. The indication may be in the form of a generated schedulethat may be viewed by an operator. Further, the indication may be atext-based indication or an alarm. In other embodiments, the indicationmay be an output sent to an automatic sample loading system.

The techniques may also be applied to more complex systems that includemultiple sequencing devices and multiples samples. FIG. 5 is a flowdiagram of a method 160 that includes the steps of receiving sequencingdevice information from a plurality of sequencing devices at block 162and receiving sample information from a plurality of samples at block164. The method 160 determines the availability of each sequencingdevice at block 166. The availability may be based on a signal from aparticular sequencing device 16 or, in particular embodiments a lack ofa signal. That is, an unavailable sequencing device 16 may send a signalwhile a sequencing run is in progress. The lack of any such signal maybe an indication that the device 16 is available. In other embodiments,the sequencing device may send an estimated availability time based onan estimated time of completion of an ongoing sequencing run. The method160 also determines a sequencing schedule based on sample information,such as a desired assay type, at block 168. At block 170, the method 160compares the desired assay type for each sample to the sequencingcapabilities of the sequencing devices 16. Finally, the method 160generates a sequencing schedule for the samples based on theavailability, the desired assay type, and any priority designation forthe samples based on the scheduling instructions, including weightingfor particular factors, at block 172.

In a particular embodiment, the system 10 may provide overrideinstructions for a case in which no sequencing devices 16 are availablefor a high priority sample, as illustrated in FIG. 6. The method 180begins with the system 10 receiving information about an ongoing runfrom an unavailable sequencing device at block 182. The method 180further receives information about the sequencing data generated by thesequencing device 16 at block 184 and an estimated time of completion atblock 186. In one embodiment, the sequencing device 16 generatesnucleotide identity files on a rolling basis as the run progresses.Genome assembly based on the nucleotide identity files may be completedeven before the sequencing run is complete if sufficient information hasbeen collected. That is, genome sequencing may generate a certainpercentage of redundant sequencing data. However, a genome may beassembled from an incomplete set of nucleotide identity files ifsufficient data has been collected. In particular embodiments, thesequencing device 16 may perform the assessment of whether sufficientdata has been collected for the assay in question. In other embodiments,the nucleotide identity files may be sent to the controller 12, and thecontroller 12 may perform the assessment. The assessment may be based onan attempt to assemble at least a portion of the genome from a minimumfile set. In other embodiments, the assessment may be based on empiricalobservation of a minimum run time or percentage completion of a run toachieve a sufficient data set. For example, the system 10 may include alook up table of a percentage of minimum completion for types oforganisms and particular assays. In such a case, i.e., if sufficientdata has been collected to achieve a desired assay result, if the sampleis high priority (block 190), the sample may be assigned to thesequencing device 16 that is in use (e.g., theoretically not available)at block 192 and the method 180 provides an indication that the ongoingrun should be interrupted at block 194 so that the higher prioritysample can be loaded into the device 16. Otherwise, for lower prioritysamples in the queue, even if the collected data set is sufficient orrepresents a minimum required set, the sequencing run is permitted torun to completion and the method 180 returns to block 182. That is,sequencing runs may be interrupted only for high priority samples and,in particular embodiments, only if sufficient data has been collectedfrom the run.

In another embodiment, the override instructions may provideinstructions to load a high priority sample alongside the sample of anongoing run, as illustrated in FIG. 7. The method 200 beings with thesystem 10 receiving information about an ongoing run from an unavailablesequencing device at block 202. The method 200 further receivesinformation about a sample density of the sample being sequenced atblock 204. If the ongoing samples is applied at low density (block 206),the device may be available for high priority samples (block 208). Ifboth conditions are true, the sample is assigned to the device 16 atblock 210 and an indication is provided that the sample should beapplied alongside the sample being sequenced. Depending on thecharacteristics of the ongoing sample and the high priority sample, thehigh priority sample may be tagged to distinguish the sample from theongoing run. Further, the samples may be related (e.g., from the sameorganism or individual) or unrelated (e.g., different organisms orindividuals). For example tagging may occur via the Multiplexing SamplePreparation Oligonucleotide Kit (Illumina) Such an embodiment may takeadvantage of a sequencing run that is plated at low density, which mayoccur if a control library is being sequenced or for low diversitysamples (e.g., expression studies with an overrepresentation of one typeof transcript, amplicon pools, adapter dimer, and initial cycleindexing). In one embodiment, a high throughput lab may keep one device16 with samples plated at low density at all times to serve as anoverflow machine for incoming high priority samples.

In another embodiment, the system 10 may schedule runs of a certain typetogether. For example, for a scheduled whole genome or a wholechromosome sequencing run, a device 16 may hold the run until enoughsamples are loaded. In one embodiment, the samples may representdifferent individuals.

Other scheduling considerations for the controller 12 may include loadbalancing. FIG. 8 is a flow diagram of a method 220 for shiftingprocessing loads based on a total processing burden of the system 10.After a sequencing schedule has been generated according to thetechniques described herein (block 222), a total processing load may beestimated that follows the sequencing schedule (block 224). Theprocessing load per sequencing device 16 may be estimated based on avariety of factors, including manufacturer specifications, sample type,assay type, duration of sequencing run, and/or density of plating. Theprocessing load of the entire system 10 is based on the combinedprocessing load of the individual sequencing devices 16 within thesystem 10 and may vary as the use of each sequencing device 16 changesover time according to the generated sequencing schedule. Because highprocessing loads may be costly, it may be advantageous to distribute theprocessing load between local sequencing devices 16 and a cloudcomputing environment if the processing load exceeds a certainthreshold. In one embodiment, the system 10 provides instructions tosequencing devices 16 that are in communication with the cloud toperform data analysis in the cloud (block 226), thus reducing the localprocessing load. Such instructions may be provided automatically upongeneration of the sequencing schedule and a determination that theestimated processing load exceeds a desirable threshold for a particulartime period.

In particular embodiments, the processing load, including anyavailability of cloud-based processing resources, may be a factor usedin determining the sequencing schedule. For example, the sequencingschedule may be optimized to smooth the processing load over time. Inother embodiment, the sequencing schedule may be optimized to shifthigher processing loads to times when processing power may be cheaper(e.g., at night).

As described herein, the system 10 generates a sequencing schedule toaccommodate a queue of biological samples. The sequencing schedulereduces operator decision making and optimizes efficient use ofresources. In particular embodiments of the disclosure, one or moresequencing devices 16 may also be used in conjunction with an automaticsample distribution system 300, as illustrated diagrammatically in FIG.9. The sample distribution system 300 may be used either as a standalonesystem or in conjunction with the sequence scheduling system 10.Further, while certain embodiments may depict sample loadingimplementations, the disclosed techniques may also be used to loadsamples and/or assay cartridges. That is, the loading may be implementedon a per-cartridge basis. The sample distribution system 300 includes asample holder or rack 302 with individual sample slots 304. Each sampleslot 304 is in fluid communication with respective conduits 306. As usedherein, the term “fluid communication” or “fluidically coupled” refersto two spatial regions being connected together such that a liquid orgas may flow between the two spatial regions. The terms “in fluidcommunication” or “fluidically coupled” allow for two spatial regionsbeing in fluid communication through one or more valves, restrictors, orother fluidic components that are configured to control or regulate aflow of fluid through the system 300. The system 300 may include one ormore pumps or pneumatic devices to pull fluid through the system in thedirection of the sequencing device 16.

The respective conduits 306 are coupled to a fluid junction 308 thatincludes a valve or other one-way control. The fluid junction 308 allowsthe fluid from only one of the conduits 306 to enter an inlet path 310at a particular time. The inlet path 310 is in fluid communication witha sample loading port of the sequencing device 16. Accordingly, when thefluid junction 308 is coupled to a specific conduit 306, the sample froma single sample slot 304 is allowed to enter the inlet path 310. Thefluid junction 308 may be coupled to a sample controller 311, whichincludes a processor 312, a memory architecture 314 storing executableinstructions 316. In specific embodiments, the sample controller 311 mayinclude operator input/output controls 318 and a display 320.Accordingly, an operator may specify that a sample is ready to be loadedinto the sequencing device and provide instructions to the fluidjunction 308 via the sample controller 311 to allow the sample to enterthe inlet path 310 and the sequencing device 16. In one example, thesample controller 311 may be implemented together with the schedulingcontroller 12 (see FIG. 1) to provide automatic distribution ofscheduled samples to assigned devices.

In one embodiment of the present techniques, multiple samples may bequeued in the inlet path 310. For example, the fluid junction may permitentry of the sample from one conduit 306, then close that pathway andallow entry of a second sample. The pathway may be cleaned betweensamples via a cleaning fluid reservoir 324. The sample controller 311may control access of the cleaning fluid to the inlet path 310. In oneexample, a sample queue in the inlet path 310 may be separated by acleaning fluid, such as a detergent, oil, or a combination thereof.

As illustrated, the sequencing device 16 may include one or morecartridges, such as a sample preparation cartridge 320 and a sequencingdata acquisition cartridge 322. The sample enters the sample preparationcartridge 320, is prepared according to the specific configuration andreagents available in the cartridge 320, and enters the sequencing dataacquisition cartridge 322 to be, for example, plated and imaged duringcluster generation in a particular embodiment. In the depictedembodiment, the sample may be applied to the sample slot without beingprepared for a particular assay. In other embodiments, the samplepreparation may occur being the sample enters the system 300. Further,the sequencing device may not include any sample preparation cartridge320. However, providing a sample preparation cartridge 320 housed withinthe sequencing device 16 may allow a particular sample to be separatedto undergo multiple assays in parallel.

For example, the sample distribution system 300 may be used inconjunction with multiple sequencing devices 16 and to apply multiplesamples to the devices 20. FIG. 10 is a diagrammatic view of a rackconfiguration having a cabinet or carriage 340 with a plurality ofsequencing devices loaded thereon. The cabinet 340 may include one ormore shelves 342 that define one or more reception spaces 344 configuredto receive the sequencing devices 16. Although not shown, the sequencingdevices 16 may be communicatively coupled to a communication networkthat permits a user to control operation of the sequencing devices 16.The sequencing devices 16 may also be coupled to the system 10 forsample scheduling.

Further, it is envisioned that the sample distribution system 300 may beinteroperable with various types of sequencing devices. To that end, thesample distribution system may be implemented as a fluidic backplanethat is sized and shaped to plug onto the sample insertion side of thesequencing devices 16. FIG. 11 shows an example of one implementation ofbackplane 350 that includes a housing 352 and a coupler 354 for theinlet path 310. The coupler 354 is designed to plug into a sampleloading port of a sequencing device 16. A sample distribution system 300may include one or more backplanes 350. In one embodiment, the backplane350 may be sized and shaped to form a side of a cabinet 340 (see FIG.10). That is, the backplane 350 may be coupled to the cabinet 340 andthe sequencing devices 16 interface with the backplane while positionedin the cabinet 340. The backplane 350 may include one or more electricalconnectors and identification features. For example, the backplane 350may include a USB connector configured to mate to a USB port on thesequencing device 16.

While only certain features of the invention have been illustrated anddescribed herein, many modifications and changes will occur to thoseskilled in the art. It is, therefore, to be understood that the appendedclaims are intended to cover all such modifications and changes as fallwithin the true spirit of the invention.

The invention claimed is:
 1. A sequencing device, comprising: a sampledevice configured to receive a biological sample and process thebiological sample during a sequencing run; a detection module coupled tothe sample device, wherein the detection module comprises detectioncircuitry configured to acquire sequence data representative ofnucleotide identities from the biological sample during the sequencingrun; and at least one processor programmed to: receive the sequence dataas the sequencing run is in progress; determine the nucleotideidentities of the biological sample based on the sequence data; generateone or more files comprising the nucleotide identities; analyze thenucleotide identities to determine if the acquired sequence data fromthe biological sample is sufficient; and provide an indication that thesequencing device is available in response to determining that thesequence data from the biological sample is sufficient to determine acharacteristic of the biological sample, wherein the indication isprovided while the detection module is acquiring additional sequencedata from the biological sample during the sequencing run and before thesequencing run is complete; wherein the processor is programmed toreassign the detection module to sequence a second biological sampleafter sufficient sequence data from the biological sample has beenacquired and before the sequencing run is complete.
 2. The sequencingdevice of claim 1, wherein the processor is programmed to receiveinstructions to communicate the nucleotide identities to a cloud-basedcomputing environment.
 3. The sequencing device of claim 1, wherein thesequencing device is communicatively coupled to a network of sequencingdevices.
 4. The sequencing device of claim 3, wherein the network ofsequencing devices comprises a distributed control system forcontrolling the sequencing devices.
 5. The sequencing system of claim 3,wherein the network of sequencing devices comprises a central controlsystem for controlling the sequencing devices.
 6. The sequencing deviceof claim 1, wherein the sample device comprises a housing having asample input port configured to receive the biological sample.
 7. Thesequencing device of claim 1, wherein the processor is programmed todetermine that the acquired sequence data is sufficient to assemble agenome of the biological sample.
 8. The sequencing device of claim 1,wherein the acquired sequence data comprises an incomplete set ofnucleotide identity files of the biological sample.
 9. The sequencingdevice of claim 1, wherein the processor is programmed to determine thatthe acquired sequence data is sufficient based on a presence of aminimum file set in the acquired sequence data.
 10. The sequencingdevice of claim 1, wherein the processor is programmed to determine thatthe acquired sequence data is sufficient based on a determination of apercentage completion of the sequencing run.
 11. The sequencing deviceof claim 10, wherein the percentage completion associated withsufficient acquired sequence data is associated with an organism oforigin of the biological sample.
 12. The sequencing device of claim 1,wherein the processor is programmed to provide instructions to thedetection module to interrupt the sequencing run before the sequencingrun is complete in response to determining that the sequence data issufficient.
 13. A sequencing device, comprising: a sample deviceconfigured to receive a biological sample and process the biologicalsample during a sequencing run; a detection module coupled to the sampledevice, wherein the detection module comprises detection circuitryconfigured to acquire sequence data representative of nucleotideidentities from the biological sample during the sequencing run; and atleast one processor programmed to: receive the sequence data as thesequencing run is in progress; determine the nucleotide identities ofthe biological sample based on the sequence data; generate one or morefiles comprising the nucleotide identities; analyze the nucleotideidentities to determine if the acquired sequence data from thebiological sample is sufficient; and provide an indication that thesequencing device is available in response to determining that thesequence data from the biological sample is sufficient to determine acharacteristic of the biological sample, wherein the indication isprovided while the detection module is acquiring additional sequencedata from the biological sample during the sequencing run and before thesequencing run is complete; wherein the processor is programmed todetermine a priority of a second biological sample in queue behind thebiological sample and to provide instructions to the detection module tointerrupt the sequencing run before the sequencing run is complete inresponse to determining that the sequence data is sufficient and thatthe priority of the second biological sample is higher than a priorityof the biological sample.
 14. The sequencing device of claim 13, whereinthe processor is programmed to receive instructions to communicate thenucleotide identities to a cloud-based computing environment.
 15. Thesequencing device of claim 13, wherein the sequencing device iscommunicatively coupled to a network of sequencing devices.
 16. Thesequencing device of claim 15, wherein the network of sequencing devicescomprises a distributed control system for controlling the sequencingdevices.
 17. The sequencing system of claim 15, wherein the network ofsequencing devices comprises a central control system for controllingthe sequencing devices.
 18. The sequencing device of claim 13, whereinthe sample device comprises a housing having a sample input portconfigured to receive the biological sample.
 19. The sequencing deviceof claim 13, wherein the processor is programmed to determine that theacquired sequence data is sufficient to assemble a genome of thebiological sample.
 20. The sequencing device of claim 13, wherein theacquired sequence data comprises an incomplete set of nucleotideidentity files of the biological sample.
 21. The sequencing device ofclaim 13, wherein the processor is programmed to determine that theacquired sequence data is sufficient based on a presence of a minimumfile set in the acquired sequence data.
 22. The sequencing device ofclaim 13, wherein the processor is programmed to determine that theacquired sequence data is sufficient based on a determination of apercentage completion of the sequencing run.
 23. The sequencing deviceof claim 22, wherein the percentage completion associated withsufficient acquired sequence data is associated with an organism oforigin of the biological sample.
 24. A sequencing device, comprising: asample device configured to receive a biological sample and process thebiological sample during a sequencing run; a detection module coupled tothe sample device, wherein the detection module comprises detectioncircuitry configured to acquire sequence data representative ofnucleotide identities from the biological sample during the sequencingrun; and at least one processor programmed to: receive the sequence dataas the sequencing run is in progress; determine the nucleotideidentities of the biological sample based on the sequence data; generateone or more files comprising the nucleotide identities; analyze thenucleotide identities to determine if the acquired sequence data fromthe biological sample is sufficient; and provide an indication that thesequencing device is available in response to determining that thesequence data from the biological sample is sufficient to determine acharacteristic of the biological sample, wherein the indication isprovided while the detection module is acquiring additional sequencedata from the biological sample during the sequencing run and before thesequencing run is complete; wherein the processor is programmed todetermine a priority of a second biological sample in queue behind thebiological sample and to provide instructions to the detection module topermit the sequencing run to run to completion in response todetermining that the sequence data is sufficient and that the priorityof the second biological sample is lower than a priority of thebiological sample.
 25. The sequencing device of claim 24, wherein theprocessor is programmed to receive instructions to communicate thenucleotide identities to a cloud-based computing environment.
 26. Thesequencing device of claim 24, wherein the sequencing device iscommunicatively coupled to a network of sequencing devices.
 27. Thesequencing device of claim 26, wherein the network of sequencing devicescomprises a distributed control system for controlling the sequencingdevices.
 28. The sequencing system of claim 26, wherein the network ofsequencing devices comprises a central control system for controllingthe sequencing devices.
 29. The sequencing device of claim 24, whereinthe sample device comprises a housing having a sample input portconfigured to receive the biological sample.
 30. The sequencing deviceof claim 24, wherein the processor is programmed to determine that theacquired sequence data is sufficient to assemble a genome of thebiological sample.
 31. The sequencing device of claim 24, wherein theacquired sequence data comprises an incomplete set of nucleotideidentity files of the biological sample.
 32. The sequencing device ofclaim 24, wherein the processor is programmed to determine that theacquired sequence data is sufficient based on a presence of a minimumfile set in the acquired sequence data.
 33. The sequencing device ofclaim 24, wherein the processor is programmed to determine that theacquired sequence data is sufficient based on a determination of apercentage completion of the sequencing run.
 34. The sequencing deviceof claim 33, wherein the percentage completion associated withsufficient acquired sequence data is associated with an organism oforigin of the biological sample.